OK, To summurize:
1. I calculate the Ctot(t) with g_rotacf using N-H index files.
2. Use trjconv to get a trajectory of internal motions.
= How I get the Cint(t)???
3. Crot = Ctot/Cint
But, is there any way to calculate the Crot(t) directly? Is trjconv the
solution again?
regards,
On 2010-09-23 21.10, Paymon Pirzadeh wrote:
OK, To summurize:
1. I calculate the Ctot(t) with g_rotacf using N-H index files.
2. Use trjconv to get a trajectory of internal motions.
= How I get the Cint(t)???
3. Crot = Ctot/Cint
But, is there any way to calculate the Crot(t) directly?
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t)
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
Yes.
2. In a paper that I just read, JCP vol. 131 155103
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some
On 2010-09-23 20.38, Paymon Pirzadeh wrote:
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
compute the rmsd. something different. I said trjconv.
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14,
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
Paymon
On Wed,
Hmm... Rotational time..? If you need diffusion constant, just use
g_rotacf and then integrate the resulting VACF. If I recall correctly,
you should make an index file with three numbers to define two vectors
for the calculation.
On Wed, Sep 22, 2010 at 7:27 PM, Paymon Pirzadeh
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